Malabsorption syndrome is a digestive disorder that prevents your body from effectively absorbing nutrients from your food. It has many causes, but most of them involve damage to the mucous lining of your small intestine, where most absorption happens.


What is malabsorption?

Malabsorption is an umbrella term for a wide range of disorders that affect your ability to absorb nutrients from your food. Malabsorption can lead to indigestion and even malnutrition — not from a lack of eating enough nutrients, but from an inability to absorb them.

You can think of digestion as a three-part process. The first part is breaking down food into digestible pieces. The second part is absorbing all the nutrients in your food. And the third part is eliminating the waste that is left over when all the good stuff has been absorbed.

If you have digestive difficulties, the problem could be in any of these three stages (or several). Malabsorption disorders cover the second stage. They include specific food intolerances caused by enzyme deficiencies, as well as various gastrointestinal diseases that affect your digestive system.


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What happens if you have malabsorption?

You can have general malabsorption, which affects your ability to absorb all nutrients, or you can have particular difficulties absorbing certain kinds of nutrients. Whatever you can’t absorb will pass undigested in your stools. People with malabsorption syndrome often have diarrhea as a side effect, which can make malabsorption worse. With diarrhea, food moves too fast through your bowels for nutrients to be absorbed.

In the short term, malabsorption will cause gastrointestinal distress from the inability to digest certain foods. Over time, your body will start to show signs of deficiency in those nutrients that you can’t absorb. Deficiencies in any of the macronutrients — protein, fats or carbohydrates — will cause signs of undernutrition, such as muscle wasting and reduced immunity. Deficiencies in micronutrients — vitamins and minerals — may affect your eyes, bones, skin and hair.

What are the different types of malabsorption disorders?

Some gastrointestinal diseases, such as celiac disease and inflammatory bowel disease, cause general malabsorption of all kinds of nutrients. In other cases, you may have particular difficulties absorbing a particular kind of nutrient. Some of these types include:

Carbohydrate malabsorption

Some people are sensitive to one or several carbohydrates (sugars). You may experience this primarily as gas pain and abdominal bloating. Carbohydrates that aren’t fully absorbed in your small intestine get fermented by the bacteria in your colon. The bacteria break them down into gasses and short-chain fatty acids. The gasses cause intestinal gas, and the short-chain fatty acids cause fatty stools.

Fat malabsorption

This is a common type of malabsorption, possibly because it has so many causes. Fats that aren’t absorbed in your small intestine pass to your colon, causing fatty stools (steatorrhea). Fatty stools are greasy and runny and particularly smelly. They may be light-colored and float. Fat malabsorption also leads to the malabsorption of fat-soluble vitamins (A, D, E and K).

Bile acid malabsorption

Sometimes fat malabsorption results from a lack of bile from diseases of the gallbladder, bile ducts or liver. But sometimes it results from another problem, leaving leftover bile acids in your small intestine and passing these on to your colon. This side effect is called bile acid malabsorption. Leftover bile salts trigger your colon to secrete water, causing chronic diarrhea.

Protein malabsorption

Protein malabsorption doesn’t usually occur by itself unless you have a particular intolerance. Examples of this include milk protein intolerances and gluten intolerance.


Symptoms and Causes

What are the symptoms of malabsorption syndrome?

Malabsorption syndrome will look like indigestion at first, with symptoms such as:

Over time, signs of malnutrition will appear.

Macronutrient undernutrition can look like:

Micronutrient undernutrition can appear as:

What are the main causes of malabsorption syndrome?

You may have temporary malabsorption during a bout of stomach flu, but malabsorption disorders that last a long time occur from an underlying condition that you’ve had for a long time. Malabsorption has many causes, but they fall into a few general categories.

Damage to the lining of the small intestine

Your small intestine is where most of your nutrient absorption happens. (A small amount happens in your large intestine.) The mucous lining of your intestinal walls is involved in both secreting digestive enzymes and absorbing liquefied food into your bloodstream. But inflammation (enteritis) and injury can damage this mucous membrane. The damage can be temporary (acute) or long-lasting (chronic). Some causes include:

Pancreas, gallbladder and liver diseases

Your pancreas, liver and gallbladder all work together with the small intestine to break down food. Your pancreas makes important digestive enzymes, while your liver and gallbladder make and store bile, which is important for digesting fats. These organs deliver their substances to your small intestine when food is present. But if a disease stops them from doing their jobs, your small intestine won’t be able to break food down enough to absorb it. Examples include:

Lymphatic system diseases

Your small intestine absorbs fats into your bloodstream through lymph vessels. Diseases of the lymphatic system that block these vessels can compromise the absorption of fats. Intestinal lymphangiectasia and lymphoma are two examples of this.

Food intolerances

Malabsorption of certain carbohydrates or proteins can occur as a side effect of gastrointestinal disease. (Fructose malabsorption is a common example.) But sometimes people are born lacking the necessary enzymes to break down certain nutrients. (Lactose intolerance is the most common example of this.)


Diagnosis and Tests

How do you know if you have malabsorption?

As with many gastrointestinal diseases, diagnosing malabsorption can be a process. Your healthcare provider will begin by examining you and considering your health history and symptoms. If you have a known history of chronic gastrointestinal disease or surgery, that may raise suspicions of malabsorption.

Some symptoms, such as fatty stools and chronic diarrhea, or evident anemia and muscle wasting, are highly suggestive of malabsorption and malnutrition. Other cases may be more subtle. Your healthcare provider will follow up with appropriate tests to narrow down the causes of your distress.

What tests are used to diagnose malabsorption?

  • Breath tests. A hydrogen breath test can help diagnose specific carbohydrate intolerances, such as lactose intolerance, as well as general small intestinal bacterial overgrowth.
  • Stool tests. A stool test can measure the fat content in your stools to diagnose fat malabsorption. It can also reveal parasitic infections, and it can show evidence of decreased pancreatic function.
  • Blood tests. These can show specific nutrient deficiencies that may result from malabsorption, as well as markers of specific conditions such as celiac disease.
  • Sweat test. This is a specific test for cystic fibrosis.
  • Imaging tests. Your healthcare provider may want to have a look at your digestive organs to look for signs of disease. They might take a GI X-ray exam, endoscopic ultrasound or video capsule endoscopy.
  • Small intestinal biopsy. Your healthcare provider may want to take a sample of small intestinal tissue to test in the lab. A biopsy can help show evidence of damage to the mucosa. They can take a sample during an endoscopic exam.

Management and Treatment

How is malabsorption syndrome treated?

Malabsorption syndrome can have many underlying causes and also a wide range of effects. Your treatment will be based on these factors.

To treat the effects of malabsorption, you may need supplemental nutrition, either in an oral formula, by tube or through a vein. You may need specific digestive enzymes replaced, either to treat a food intolerance or general pancreatic insufficiency. If you have bile acid malabsorption, you may need bile acid sequestrants (food additive) to help prevent diarrhea.

Treating the underlying cause of malabsorption can be more complicated. If it’s only from a food intolerance, you may simply have to adjust your diet. Simple infections can be treated with antibiotics. But chronic diseases will require more particular treatment. Sometimes there is no direct cure, but lifestyle adjustments can help relieve symptoms.

Outlook / Prognosis

Does malabsorption go away?

This depends on effectively diagnosing and treating the cause. Some causes are more treatable than others. Your healthcare provider will fill you in on the details of your prognosis when you have been diagnosed. In many cases, you can help treat malabsorption and its symptoms with lifestyle changes.

A note from Cleveland Clinic

Most people experience occasional indigestion, bloating, gas or diarrhea. If something you eat doesn’t agree with you, you may have temporary symptoms, but they typically go away on their own. This type of indigestion is usually no cause for real concern. But if you have chronic symptoms, there may be something larger going on. Persistent diarrhea in particular should always be taken seriously.

Malabsorption can be a hidden cause of malnutrition. Since malnutrition occurs gradually, you might not notice it until it is advanced, especially if you have an adequate diet. This is especially dangerous for children, who have higher nutritional needs to support their growth and development, and who may not know how to tell you about their symptoms. If your child shows signs of recurring gastrointestinal distress, especially loose stools, make sure to see your healthcare provider to rule out malabsorption.

Medically Reviewed

Last reviewed on 04/06/2022.

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